MolNFT v1 · #122114 · protein
Purine nucleoside phosphorylase
5IFK: “Purine nucleoside phosphorylase”. X-ray diffraction, 1 ligand (HPA), 4 pockets (best druggability 0.62). MolNFT v1 #122114 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IFK
- Type
- protein
- Length
- 880 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- Q6CSZ6
- Ligands
- HPA
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 295 | 35% helix, 22% strand | Q6CSZ6 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 293 | 35% helix, 22% strand | Q6CSZ6 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 292 | 36% helix, 22% strand | Q6CSZ6 |
Ligands and binding sites
- HPA · Hypoxanthine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.62 | 0.82 | 35 | HPA |
| 2 | 218 | 0.62 | 0.82 | 31 | HPA |
| 3 | 415 | 0.62 | 0.77 | 71 | empty |
| 4 | 212 | 0.62 | 0.82 | 35 | HPA |
Interfaces
3 interfaces between chains.
- B–C · 1615 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1613 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1613 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5IFK · Purine nucleoside phosphorylase · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6CSZ6
- Elsewhere: RCSB PDB 5IFK · PDBe 5IFK · UniProt Q6CSZ6
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